ENST00000518540.5:n.416-28624G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000518540.5(LINC01592):​n.416-28624G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,038 control chromosomes in the GnomAD database, including 25,290 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.55 ( 25290 hom., cov: 32)

Consequence

LINC01592
ENST00000518540.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0510

Publications

3 publications found
Variant links:
Genes affected
LINC01592 (HGNC:51557): (long intergenic non-protein coding RNA 1592)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC01592NR_039986.1 linkn.416-28624G>A intron_variant Intron 2 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC01592ENST00000518540.5 linkn.416-28624G>A intron_variant Intron 2 of 4 2
LINC01592ENST00000519062.7 linkn.149+18598G>A intron_variant Intron 1 of 3 3
LINC01592ENST00000524286.2 linkn.166+15518G>A intron_variant Intron 2 of 4 3

Frequencies

GnomAD3 genomes
AF:
0.547
AC:
83147
AN:
151920
Hom.:
25231
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.827
Gnomad AMI
AF:
0.470
Gnomad AMR
AF:
0.502
Gnomad ASJ
AF:
0.436
Gnomad EAS
AF:
0.491
Gnomad SAS
AF:
0.625
Gnomad FIN
AF:
0.362
Gnomad MID
AF:
0.579
Gnomad NFE
AF:
0.422
Gnomad OTH
AF:
0.516
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.548
AC:
83267
AN:
152038
Hom.:
25290
Cov.:
32
AF XY:
0.546
AC XY:
40575
AN XY:
74298
show subpopulations
African (AFR)
AF:
0.827
AC:
34341
AN:
41504
American (AMR)
AF:
0.503
AC:
7675
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.436
AC:
1513
AN:
3470
East Asian (EAS)
AF:
0.491
AC:
2533
AN:
5162
South Asian (SAS)
AF:
0.625
AC:
3014
AN:
4820
European-Finnish (FIN)
AF:
0.362
AC:
3825
AN:
10564
Middle Eastern (MID)
AF:
0.571
AC:
168
AN:
294
European-Non Finnish (NFE)
AF:
0.422
AC:
28687
AN:
67942
Other (OTH)
AF:
0.513
AC:
1083
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1708
3415
5123
6830
8538
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
684
1368
2052
2736
3420
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.450
Hom.:
25800
Bravo
AF:
0.567
Asia WGS
AF:
0.548
AC:
1902
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.2
DANN
Benign
0.34
PhyloP100
-0.051

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs7825569; hg19: chr8-69895021; API